LOCUS       NZ_CP050767             3373 bp    DNA     circular CON 03-JUN-2024
DEFINITION  Salmonella enterica subsp. enterica serovar Indiana strain SI111
            plasmid pSI111-3, complete sequence.
ACCESSION   NZ_CP050767
VERSION     NZ_CP050767.1
DBLINK      BioProject: PRJNA224116
            BioSample: SAMN14450156
            Assembly: GCF_012053145.1
KEYWORDS    RefSeq.
SOURCE      Salmonella enterica subsp. enterica serovar Indiana
  ORGANISM  Salmonella enterica subsp. enterica serovar Indiana
            Bacteria; Pseudomonadota; Gammaproteobacteria; Enterobacterales;
            Enterobacteriaceae; Salmonella.
REFERENCE   1  (bases 1 to 3373)
  AUTHORS   Chen,Z.
  TITLE     Genomic analyses of multidrug-resistant Salmonella Indiana,
            Typhimurium, and Enteritidis isolates using MinION and MiSeq
            sequencing technologies
  JOURNAL   Unpublished
REFERENCE   2  (bases 1 to 3373)
  AUTHORS   Chen,Z.
  TITLE     Direct Submission
  JOURNAL   Submitted (26-MAR-2020) Joint Institute for Food Safety and Applied
            Nutrition, University of Maryland, 5145 Campus Drive, Patapsco
            Building, Suite 2134, College Park, MD 20742, USA
COMMENT     ##Genome-Assembly-Data-START##
            Assembly Method                   :: Unicycler v. 0.4.8
            Assembly Name                     :: SI111
            Genome Representation             :: Full
            Expected Final Version            :: Yes
            Genome Coverage                   :: 124x
            Sequencing Technology :: Illumina MiSeq; Oxford Nanopore MiniION
            ##Genome-Assembly-Data-END##
            ##Genome-Annotation-Data-START##
            Annotation Provider               :: NCBI RefSeq
            Annotation Name                   :: GCF_012053145.1-RS_2024_06_03
            Annotation Date                   :: 06/03/2024 02:25:48
            Annotation Pipeline :: NCBI Prokaryotic Genome Annotation Pipeline
            (PGAP)
            Annotation Method :: Best-placed reference protein set; GeneMarkS-2+
            Annotation Software revision      :: 6.7
            Features Annotated                :: Gene; CDS; rRNA; tRNA; ncRNA
            Genes (total)                     :: 4,787
            CDSs (total)                      :: 4,669
            Genes (coding)                    :: 4,503
            CDSs (with protein)               :: 4,503
            Genes (RNA)                       :: 118
            rRNAs                             :: 8, 7, 7 (5S, 16S, 23S)
            complete rRNAs                    :: 8, 7, 7 (5S, 16S, 23S)
            tRNAs                             :: 84
            ncRNAs                            :: 12
            Pseudo Genes (total)              :: 166
            CDSs (without protein)            :: 166
            Pseudo Genes (ambiguous residues) :: 0 of 166
            Pseudo Genes (frameshifted)       :: 61 of 166
            Pseudo Genes (incomplete)         :: 125 of 166
            Pseudo Genes (internal stop)      :: 35 of 166
            Pseudo Genes (multiple problems)  :: 46 of 166
            CRISPR Arrays                     :: 2
            ##Genome-Annotation-Data-END##
            REFSEQ INFORMATION: The reference sequence is identical to
            CP050767.1.
            The annotation was added by the NCBI Prokaryotic Genome Annotation
            Pipeline (PGAP). Information about PGAP can be found here:
            https://www.ncbi.nlm.nih.gov/genome/annotation_prok/
            COMPLETENESS: full length.
FEATURES             Location/Qualifiers
     source          1..3373
                     /organism="Salmonella enterica subsp. enterica serovar
                     Indiana"
                     /mol_type="genomic DNA"
                     /strain="SI111"
                     /serovar="Indiana"
                     /isolation_source="Diarrheal patient"
                     /host="Homo sapiens"
                     /sub_species="enterica"
                     /db_xref="taxon:286783"
                     /plasmid="pSI111-3"
                     /geo_loc_name="China:Shanghai"
                     /lat_lon="31.23 N 121.47 E"
                     /collection_date="2013-11-13"
                     /collected_by="Shanghai Municipal Center for Disease
                     Control and Prevention"
     gene            complement(909..1100)
                     /locus_tag="HEC81_RS23720"
                     /old_locus_tag="HEC81_23720"
     CDS             complement(909..1100)
                     /locus_tag="HEC81_RS23720"
                     /old_locus_tag="HEC81_23720"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000165979.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="Rop family plasmid primer RNA-binding protein"
                     /protein_id="WP_000165979.1"
                     /translation="MTKQEKTALNMARFIRSQTLTLLEKLNDLDADEQADICESLHDHA
                     DELYRSCLARFGDDGESN"
                     /name="Rop family plasmid primer RNA-binding protein"
     gene            1164..1487
                     /locus_tag="HEC81_RS23725"
                     /old_locus_tag="HEC81_23725"
     CDS             1164..1487
                     /locus_tag="HEC81_RS23725"
                     /old_locus_tag="HEC81_23725"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000956000.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MobC family plasmid mobilization relaxosome
                     protein"
                     /protein_id="WP_001696562.1"
                     /translation="MLTIRVTDEEHARLLERCEGKRLAEWMRRVCLGEPVARTGKLPTL
                     APPLLRHLAAIGNNLNQTARKVNSGQWSSIDRVHVVAALMAIEGELRQLRQAVREQGVR
                     DDS"
                     /name="MobC family plasmid mobilization relaxosome protein"
     gene            1696..>2133
                     /locus_tag="HEC81_RS24140"
                     /pseudo=""
     CDS             1696..>2133
                     /locus_tag="HEC81_RS24140"
                     /inference="COORDINATES: protein motif:HMM:NF015397.4"
                     /note="incomplete; partial in the middle of a contig;
                     missing C-terminus; Derived by automated computational
                     analysis using gene prediction method: Protein Homology."
                     /pseudo=""
                     /codon_start=1
                     /transl_table=11
                     /product="relaxase/mobilization nuclease domain-containing
                     protein"
                     /name="relaxase/mobilization nuclease domain-containing
                     protein"
     gene            2165..2725
                     /locus_tag="HEC81_RS23735"
                     /old_locus_tag="HEC81_23735"
     CDS             2165..2725
                     /locus_tag="HEC81_RS23735"
                     /old_locus_tag="HEC81_23735"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000067488.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeB family mobilization protein"
                     /protein_id="WP_000067487.1"
                     /translation="MSNLLQMGTDFEKKLKERAASTENMLNSEFRKLEESVDKALSLNR
                     QKIRDAISEHTTSVKKQLDTLSTTVSMQFSTTEAELSRQQKKLLWRVIKGRILFPALTA
                     LSVTGGIFLGCWGLMEWQESKIAKNILTIREQENTLAKLEAKTWGVTFVNGENGKFLVL
                     PDGVKGENTWTVGDKNAVRLVRE"
                     /name="MbeB family mobilization protein"
     gene            2732..2965
                     /locus_tag="HEC81_RS23740"
                     /old_locus_tag="HEC81_23740"
     CDS             2732..2965
                     /locus_tag="HEC81_RS23740"
                     /old_locus_tag="HEC81_23740"
                     /inference="COORDINATES: similar to AA
                     sequence:RefSeq:WP_000137389.1"
                     /note="Derived by automated computational analysis using
                     gene prediction method: Protein Homology."
                     /codon_start=1
                     /transl_table=11
                     /product="MbeD family mobilization/exclusion protein"
                     /protein_id="WP_000137389.1"
                     /translation="MTELEGHLLNALEHLQQDYMRRLNEWESAFAELQKMHEVTQRNNA
                     ILNERVVILSQQVQRLAGQVDRLSRLFIANNS"
                     /name="MbeD family mobilization/exclusion protein"
     Typing          745..828
                     /name="MOBP"
                     /typing="oriT"
                     /tool="MOB-suite"
                     /identity="85.882"
                     /coverage="95.0"
                     /evalue="4.11e-16"
     Typing          1478..3048
                     /name="MOBP"
                     /typing="relaxase"
                     /tool="MOB-suite"
                     /identity="92.628"
                     /coverage="100.0"
                     /evalue="0.0"
ORIGIN
        1 ccagttcatt cagtttgcat gaaccttctg tattcttcaa gaatttttca acagcacagt
       61 ctcccaggaa ccccgaaaaa aacctgtttt tgcagatact tgcgtatttg cgagaatcgt
      121 ttgcggttgg gggagctgtg acgacggcga ccgcacgcgt gagagttccg ctaccggcgc
      181 agagagtttc atcgacagcg gacacctgat gagttgccac aaaaaccgta tgtagcgcgg
      241 ctagattggt tgagttagac cttggcggca gttcccggta tgtggtggcg tgacgggtga
      301 gatggtgcgg cgaagacgca tacgtcacgc aggcgcgggt tcttccactg acgcgccccg
      361 tgatcgatgg ccttggctcc gtccggcata tcgagagcgg caaactaccc gtcccttcac
      421 tgggaggggt gagttgttgc cgttccctcc gaccttccac catccagcat atcgcacgat
      481 cccatgtgca ccgctactcc tgataactcc agtgcaaaaa aaaaaacgga tctgcatcac
      541 aacgagagtg atcccgccgc tcgccgcagc cccagcgacc gaacgtagtg agcgagtggg
      601 cgaggaagcg gaagagtcac agaggcaagc attgtgcact tacgcgcctg tgccagtgtc
      661 cgcgtgtgtg ttgtttatcg ggcgcgctgt ttttacgcat ctgtgcggct ttttactcct
      721 gacatggtgc acttcccatc cactctgcac cgatgcaaaa tgaggaaagc cagtatacac
      781 atcgctatcg ctctgtgaac tgggtcaggg ctgcgccccg acacccgcac tgacgcgccc
      841 tggcgggctt gtctgctccc ggcatccgct cacaggcaag ctgtgaacgt ctccgggagc
      901 tgcatgtttc agttgctttc accgtcatcg ccgaagcgtg cgaggcaact gcggtagagt
      961 tcgtcggcgt ggtcgtgaag tgattcgcag atgtctgcct gttcgtccgc gtccagatcg
     1021 ttgagttttt ccagcagggt tagcgtctgg cttctgataa agcgagccat gttaagggct
     1081 gttttttcct gtttggtcat ggtcttaagg ctccttgtat gggggatttg ttagggggaa
     1141 tgataccgat gaaacgcgag aagatgctca cgatacgggt taccgatgag gagcacgccc
     1201 ggttactgga acgctgcgag ggtaaacgac tggcggaatg gatgcggcgg gtctgtctgg
     1261 gggagccggt tgcacgcaca ggaaaactgc cgacactggc accgccattg ctgcggcatc
     1321 tggctgccat cgggaacaac ctgaaccaga cagcccggaa ggtgaacagc ggccagtggt
     1381 cttcgattga ccgggttcat gtggtggccg cactgatggc catcgagggt gaattgcgcc
     1441 agttgcggca ggctgtcagg gaacaggggg tacgggatga tagttaaatt tcatgccagg
     1501 gggaaaggcg gtggaagtgg cccggtcgat tacctgctgg ggcgggagcg taaccgcgaa
     1561 ggcgcaacgg tgctccgggg taacccggaa gaagtgcggg aactcattga ttccacgcca
     1621 ttttcgaaga aatacacgtc aggcgttctg tcgttcgcgg agaaggagct accaccgggt
     1681 gaacgcgaaa gagtgatgac gagctttgag cgtgttctta tgcccggtct cgaaaaagac
     1741 cagtacagca ttctctgggt ggaacaccag gataaggggc ggctcgaact gaattttgtc
     1801 atcccgaaca tggagctaca gagcggtaag cgcctccagc cgtactacga ccgtgcggac
     1861 aggccgagga taaatgcctg gcagacgctg gttaatcatc attacgggct gcgtgacccg
     1921 aacgcaccgg agaacagacg gacgcttgtc acgccaaata atctgccaaa agcgaaacag
     1981 gaggccgcag aagcgattac acggggtctt gaggctcttt accatgccgg agcaataaaa
     2041 acgcgtcagg atgtcacaga ggcgcttaca gcggcaggtt ttgaggtggt gaggacaacc
     2101 aaaagcagca tcagtattgc cgacccggag ggggggcgga atctcaggct aaagggggcg
     2161 ctgtatgagc aatcttttac aaatgggaac agacttcgag aagaaactga aagagcgagc
     2221 cgcttctacc gagaacatgc tgaacagcga gttcaggaag ctcgaagagt ctgtagacaa
     2281 ggcactgagc ttaaacaggc agaaaatcag agacgctatc agcgaacata caacatccgt
     2341 gaaaaagcaa ctggatacgc tgagcaccac cgtgagcatg cagttcagca ccacagaggc
     2401 cgaactgtcc cggcagcaga aaaaactgct ctggcgggtg atcaaagggc ggatactgtt
     2461 tccggcgctg accgcgctca gcgtcacggg cgggattttc ctggggtgct gggggctgat
     2521 ggagtggcag gaaagcaaga ttgcgaaaaa tatcctgact atcagagagc aggaaaacac
     2581 gctggcgaaa ctcgaggcaa aaacctgggg ggtgacgttc gtcaatggcg agaacgggaa
     2641 atttctggtg ttgccggacg gggtgaaagg ggaaaacacc tggacggtgg gcgacaagaa
     2701 cgccgtgagg ctggtcaggg agtaaacgag aatgacggaa ctggaagggc atttgctgaa
     2761 cgccttagag catttgcaac aggactatat gcggcggctg aacgagtggg agagcgcctt
     2821 cgcggaattg cagaagatgc acgaggttac gcaacggaac aacgcgatac tgaacgagcg
     2881 cgtcgtgata ttgagtcagc aggtgcagag attagccggg caagtggatc gcttgagtcg
     2941 gttatttatc gcgaacaaca gctaagggat gaacaggagc gtgcccggta cagacatgag
     3001 gtacaggaac gcgcggcacg ggttcggagt gggccatcaa tggagatgtg accggggaag
     3061 tgacgaaatc ttgccatttt gacccgttcg acggctgggg cgagcgaaac aaatcgtgtg
     3121 ccgtatttgt gcatagctat gcaacatcct gaaaacgcat ttcacgcgtt tttggggatt
     3181 cagccagggg aaaacatggt ttttttactt tttgagcgta aagacgtgaa aaatctcgtt
     3241 attgcacttg cgatctttcg tcggcgggag tagaacgaaa acagctcgcc aggaaggcga
     3301 gctgtttcgg gttcattgag gtctctgacc tcctcaatgt tcctgtggaa actgttgaga
     3361 tccacaacag aaa
//
